Ferns belong to species-rich group of land plants, encompassing more than 11,000 extant species, and are crucial for reflecting terrestrial ecosystem changes. However, our understanding of their biodiversity hotspots, particularly in Southeast Asia, remains limited due to scarce genetic data. Despite harboring around one-third of the world's fern species, less than 6% of Southeast Asian ferns have been DNA-sequenced. In this study, we addressed this gap by sequencing 1,496 voucher-referenced and expert-identified fern samples from (sub)tropical Asia, spanning Malaysia, the Philippines, Taiwan, and Vietnam, to retrieve their rbcL and trnL-F sequences. This DNA barcode collection of Asian ferns encompasses 956 species across 152 genera and 34 families, filling major gaps in fern biodiversity understanding and advancing research in systematics, phylogenetics, ecology and conservation. This dataset significantly expands the Fern Tree of Life to over 6,000 species, serving as a pivotal and global reference for worldwide barcoding identification of ferns.